The Lower Bay Complex is a triangular body of water that is bounded by Brooklyn, the Atlantic Ocean and Sandy Hook on the east, New Jersey to the south, and Staten Island to the west (Fig. 18.1). It consists of three connected bays: Lower Bay, Raritan Bay, and Sandy Hook Bay. It is a generally shallow, well-mixed estuary, with only dredged ship channels, sand mining areas, and the region near the Narrows exceeding 8 m in depth. Annual bottom water temperatures range from about 2° to greater than 24°C. Salinity along the Sandy Hook to Rockaway Beach transect reflects coastal ocean values at 32 practical salinity units (psu) but declines by as much as 10 psu both towards the Narrows and the Raritan River. A clockwise eddy off Great Kills effectively separates the Raritan River and Hudson River flows, creating different hydro-graphic regimes in the north (Lower Bay) and south (Raritan and Sandy Hook Bays) (Jeffries, 1962). Bottom sediments cover a full range of grain sizes from coarse gravel/shell/sand areas to fine-grained muds. Sand predominates the sediments of Lower Bay, while Raritan and Sandy Hook Bays tend to be muddy.

The Lower Bay Complex receives water from the Atlantic Ocean andmixes it with fresher water coming from many regions in the New York- New Jersey Harbor area (NYCDEP, 2000). Not only is it downstream from the Hudson and Raritan Rivers, but it also receives water from Jamaica Bay, western Long Island Sound via the East River and Upper Bay, and the Passaic and Hackensack Rivers via Newark Bay, Upper Bay and Arthur Kill (NYCDEP, 2000). This water carries a wide variety of substances, including inorganic and organic nutrients, inorganic particles, living and dead organic particles, and contaminants. These substances are altered within the Lower Bay Complex by a number of physical (e.g., dilution, sedimentation), chemical (e.g., adsorption, dissolution, oxidation, reduction), and biological (e.g., ingestion, assimilation) processes. The Lower Bay Complex is also a conduit for fish migrating into and out of the New York-New Jersey Harbor region.

Within the Lower Bay Complex, the distribution of benthic animals, i.e., those animals living on or within the bottom, varies both in space and in time. Benthic species are adaptedfor an association with the substrate and hydrodynamic regime in which they live (Parsons, Takahashi, and Hargrave, 1984; Barry and Dayton, 1991). Thus, barnacles are abundant only in areas with hard surfaces such as rock or shell and adequate water flow, while deposit feeding marine worms tend to be common in muddy sediments. Additional variability in the fauna is caused by physical fluctuations that are characteristic of temperate estuaries and coastal marine

systems. Extremes in temperature, large changes in salinity, tidal scour, storm erosion, and other natural processes all represent natural disturbances that affect benthic organisms. The annual range in bottom water temperature in the Lower Bay Complex, for example, is as large as in any marine environment. Benthic communities are also patchy in space and time because of the effects of biotic factors such as competition, predation, variability in larval recruitment, and the fact that benthic organisms, especially those living in soft sediments, alter the physical and chemical properties of their associated substrate by their feeding and burrowing activities (Johnson, 1970; Rhoads, 1974; Thrush, 1991). As a result of variations in physical and biotic processes, benthic communitystructure in nearshore, temperate environments has been described as a spatial and temporal mosaic (e.g., Johnson, 1970; Rhoads, McCall, andYingst, 1978).

Anthropogenic activity adds still another source of disturbance to benthic communities in New York-New Jersey Harbor. The Lower Bay Complex is surrounded by one of the largest urban and industrial regions in the world and has been subjected to considerable anthropogenic impacts in the form of raw sewage discharges, hypoxia, oil spills, and dredging (NYCDEP, 2000). Jeffries (1962), for example, described Raritan Bay as one of the most polluted coastal areas in the United States. Most measures of sediment contaminants are higher than average in New York - New Jersey Harbor when compared to other locations in the mid-Atlantic (Adams et al., 1998).

The benthic fauna of the Lower Bay Complex has been more extensively studied than any other benthic community in the New York-New Jersey Harbor area. Several of the benthic studies (Dean, 1975; McGrath, 1974; Stainken, McCormick, and Multer, 1984; Cerrato, Bokuniewicz, and Wiggins, 1989; Adams, O'Connor, and Weisberg, 1998; NOAA-USACE, 2001) were regional in scope and attempted to cover substantial portions ofthe area (Table 18.1). Interestingly, these studies span a period of over four decades, from 1957 to 1995, providing the potential to examine both large-scale spatial and long-term temporal patterns in benthic community structure.

In this chapter, I will use those regional surveys that are the most compatible in terms of sampling methods to examine the large-scale spatial

Table 18.1. Characteristics of regional studies of the Lower Bay Complex

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